Comparative nucleotide sequences of flavivirus genomic RNA and deduced amino acid sequences of viral proteins

Abstract: Nucleotide (nt) and deduced amino acid (AA) sequences of 11 flaviviruses were compared for each genome segment based on the data of yellow fever (YF) virus. Two nonstructural proteins, NS3 and NS5, were highly conserved, while core protein (C) was least conseved among these viruses. In general, nonstructural proteins were more highly conserved than structural proteins. A consensus tripeptide sequence (Gly-Asp-Asp) of viral RNA polymerases was found almost at the same position of NS5 protein for all flaviviruses. In envelope glycoprotein (E) and NS1 protein, 12 Cys residues were conserv-ed among all flaviviruses, and E protein possessed some highly conserved regions which could be essential for its structure and function. Sequence homology among all 11 flaviviruses classified them into 3-4 subgroups, which roughly corresponded to the subgroups of classical serology. A hexapeptide sequence of Asn-Met-Leu-Lys-Arg-Gly, similar to the sequence in some uncleic acid-binding protein, was conserved for 6 of 11 flavivirus core proteins (C)